Starting phenix.real_space_refine on Tue Aug 4 15:10:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9q_65785/08_2026/9w9q_65785.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2742 2.51 5 N 702 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4254 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "A" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "F" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Time building chain proxies: 1.00, per 1000 atoms: 0.24 Number of scatterers: 4254 At special positions: 0 Unit cell: (90.21, 159.96, 34.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 804 8.00 N 702 7.00 C 2742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 151.0 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 37.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 16 removed outlier: 6.257A pdb=" N LYS D 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.062A pdb=" N ALA D 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 34 removed outlier: 6.255A pdb=" N ALA D 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL B 28 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASN D 27 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL B 30 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA D 29 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 32 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N HIS D 31 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ARG B 34 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE D 33 " --> pdb=" O ARG B 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.726A pdb=" N THR D 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.868A pdb=" N GLU D 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 67 " --> pdb=" O GLU D 66 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL D 65 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ILE E 68 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY D 67 " --> pdb=" O ILE E 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.417A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.895A pdb=" N SER D 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR B 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.390A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 92 through 98 removed outlier: 6.188A pdb=" N GLU D 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE E 95 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA E 97 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 96 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 105 through 107 removed outlier: 5.905A pdb=" N THR D 106 " --> pdb=" O ILE E 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.831A pdb=" N THR D 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 121 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA D 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.053A pdb=" N MET A 13 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL C 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS A 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 21 removed outlier: 6.765A pdb=" N VAL A 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 25 through 34 removed outlier: 6.941A pdb=" N ILE A 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ALA F 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 28 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS F 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A 30 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N PHE F 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 32 " --> pdb=" O PHE F 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 60 through 62 removed outlier: 7.007A pdb=" N THR A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 73 removed outlier: 6.246A pdb=" N GLU A 72 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.960A pdb=" N SER A 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR C 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N LYS A 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.321A pdb=" N TRP F 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TYR A 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 92 through 98 removed outlier: 6.142A pdb=" N GLU A 92 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE F 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL A 94 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA F 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR A 96 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 104 through 107 removed outlier: 6.090A pdb=" N ARG A 104 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE F 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR A 106 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.653A pdb=" N THR A 119 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL F 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 121 " --> pdb=" O VAL F 122 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1323 1.34 - 1.45: 583 1.45 - 1.57: 2432 1.57 - 1.68: 0 1.68 - 1.80: 12 Bond restraints: 4350 Sorted by residual: bond pdb=" CB ARG D 104 " pdb=" CG ARG D 104 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CB ARG E 104 " pdb=" CG ARG E 104 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.28e+00 bond pdb=" CB ARG B 104 " pdb=" CG ARG B 104 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.10e+00 bond pdb=" CB GLU F 92 " pdb=" CG GLU F 92 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" CB GLU C 92 " pdb=" CG GLU C 92 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.73e+00 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5730 1.69 - 3.39: 144 3.39 - 5.08: 27 5.08 - 6.77: 18 6.77 - 8.47: 3 Bond angle restraints: 5922 Sorted by residual: angle pdb=" C GLU E 62 " pdb=" N GLU E 63 " pdb=" CA GLU E 63 " ideal model delta sigma weight residual 121.54 127.93 -6.39 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C GLU D 62 " pdb=" N GLU D 63 " pdb=" CA GLU D 63 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" C GLU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.54 127.87 -6.33 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA GLU C 92 " pdb=" CB GLU C 92 " pdb=" CG GLU C 92 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.28e+00 angle pdb=" CA GLU A 92 " pdb=" CB GLU A 92 " pdb=" CG GLU A 92 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.27e+00 ... (remaining 5917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.02: 2148 12.02 - 24.04: 267 24.04 - 36.06: 99 36.06 - 48.07: 42 48.07 - 60.09: 30 Dihedral angle restraints: 2586 sinusoidal: 978 harmonic: 1608 Sorted by residual: dihedral pdb=" CA GLU C 66 " pdb=" C GLU C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLU F 66 " pdb=" C GLU F 66 " pdb=" N GLY F 67 " pdb=" CA GLY F 67 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 66 " pdb=" C GLU A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta harmonic sigma weight residual 180.00 162.39 17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 362 0.028 - 0.055: 167 0.055 - 0.083: 57 0.083 - 0.110: 90 0.110 - 0.138: 32 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE D 107 " pdb=" N ILE D 107 " pdb=" C ILE D 107 " pdb=" CB ILE D 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE E 107 " pdb=" N ILE E 107 " pdb=" C ILE E 107 " pdb=" CB ILE E 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 107 " pdb=" N ILE B 107 " pdb=" C ILE B 107 " pdb=" CB ILE B 107 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 705 not shown) Planarity restraints: 726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 69 " 0.017 2.00e-02 2.50e+03 1.63e-02 5.32e+00 pdb=" CG TYR C 69 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR C 69 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 69 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR C 69 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR C 69 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 69 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " 0.018 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR A 69 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 69 " 0.017 2.00e-02 2.50e+03 1.59e-02 5.05e+00 pdb=" CG TYR F 69 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 69 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR F 69 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR F 69 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR F 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 69 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 69 " -0.001 2.00e-02 2.50e+03 ... (remaining 723 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 710 2.79 - 3.31: 3598 3.31 - 3.84: 7542 3.84 - 4.37: 7972 4.37 - 4.90: 15521 Nonbonded interactions: 35343 Sorted by model distance: nonbonded pdb=" OG1 THR D 119 " pdb=" OH TYR B 114 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR D 114 " pdb=" OG1 THR E 119 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR F 119 " model vdw 2.266 3.040 nonbonded pdb=" OH TYR A 69 " pdb=" O ASN F 27 " model vdw 2.338 3.040 ... (remaining 35338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4350 Z= 0.155 Angle : 0.718 8.465 5922 Z= 0.378 Chirality : 0.052 0.138 708 Planarity : 0.004 0.032 726 Dihedral : 14.952 60.092 1542 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 22.44 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.31), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 104 TYR 0.040 0.003 TYR C 69 PHE 0.003 0.001 PHE B 33 TRP 0.002 0.001 TRP B 79 HIS 0.004 0.001 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4350) covalent geometry : angle 0.71830 / 0.38 ( 5922) hydrogen bonds : bond 0.15479 / 10.73 ( 63) hydrogen bonds : angle 9.85023 / 6.83 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.155 Fit side-chains REVERT: A 74 ASP cc_start: 0.8050 (t0) cc_final: 0.7647 (t0) REVERT: B 13 MET cc_start: 0.6018 (tpp) cc_final: 0.4297 (ttp) REVERT: B 117 SER cc_start: 0.8753 (m) cc_final: 0.8499 (t) REVERT: C 74 ASP cc_start: 0.8015 (t0) cc_final: 0.7708 (t0) REVERT: E 63 GLU cc_start: 0.7575 (pt0) cc_final: 0.7200 (tp30) REVERT: F 74 ASP cc_start: 0.8033 (t0) cc_final: 0.7493 (t0) REVERT: F 103 ARG cc_start: 0.6527 (mtm-85) cc_final: 0.4699 (mmp80) REVERT: F 116 TYR cc_start: 0.8732 (m-80) cc_final: 0.8486 (m-80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0900 time to fit residues: 8.7889 Evaluate side-chains 71 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.193938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.167926 restraints weight = 4384.213| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.13 r_work: 0.4026 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4350 Z= 0.089 Angle : 0.469 5.899 5922 Z= 0.250 Chirality : 0.048 0.127 708 Planarity : 0.003 0.023 726 Dihedral : 4.379 16.008 588 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.42 % Allowed : 20.73 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.009 0.001 TYR A 114 PHE 0.005 0.001 PHE B 95 TRP 0.003 0.001 TRP D 79 HIS 0.001 0.000 HIS D 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.09 ( 4350) covalent geometry : angle 0.46874 / 0.25 ( 5922) hydrogen bonds : bond 0.01410 / 0.95 ( 63) hydrogen bonds : angle 5.38673 / 3.70 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.090 Fit side-chains REVERT: D 104 ARG cc_start: 0.7893 (ptp-110) cc_final: 0.7394 (ptp-110) REVERT: A 12 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6951 (tt) REVERT: A 70 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8067 (tttt) REVERT: A 74 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8054 (t0) REVERT: B 111 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 13 MET cc_start: 0.6511 (mmm) cc_final: 0.6118 (mmm) REVERT: C 15 LYS cc_start: 0.8595 (tttt) cc_final: 0.8357 (tttm) REVERT: E 104 ARG cc_start: 0.7379 (ptp-110) cc_final: 0.7132 (ttp-170) REVERT: F 12 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7281 (tt) REVERT: F 69 TYR cc_start: 0.8722 (m-80) cc_final: 0.8410 (m-80) REVERT: F 74 ASP cc_start: 0.8391 (t0) cc_final: 0.7942 (t0) REVERT: F 103 ARG cc_start: 0.6908 (mtm-85) cc_final: 0.5153 (mmp80) outliers start: 16 outliers final: 6 residues processed: 84 average time/residue: 0.0643 time to fit residues: 6.5577 Evaluate side-chains 76 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain F residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.156878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129435 restraints weight = 4908.670| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.18 r_work: 0.3628 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 4350 Z= 0.337 Angle : 0.689 5.193 5922 Z= 0.374 Chirality : 0.054 0.145 708 Planarity : 0.005 0.045 726 Dihedral : 5.532 19.948 588 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.84 % Allowed : 19.23 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 103 TYR 0.024 0.003 TYR A 114 PHE 0.012 0.003 PHE E 33 TRP 0.010 0.003 TRP A 79 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00776 / 0.34 ( 4350) covalent geometry : angle 0.68906 / 0.37 ( 5922) hydrogen bonds : bond 0.02468 / 1.57 ( 63) hydrogen bonds : angle 5.12208 / 3.61 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 76 time to evaluate : 0.150 Fit side-chains REVERT: D 85 SER cc_start: 0.8904 (t) cc_final: 0.8588 (p) REVERT: D 104 ARG cc_start: 0.7824 (ptp-110) cc_final: 0.7116 (ptp-110) REVERT: A 12 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6906 (tt) REVERT: A 15 LYS cc_start: 0.8897 (tttt) cc_final: 0.8357 (ttmt) REVERT: E 63 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: E 74 ASP cc_start: 0.8125 (t0) cc_final: 0.7923 (t70) REVERT: E 103 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: E 104 ARG cc_start: 0.7505 (ptp-110) cc_final: 0.7247 (ttp-170) REVERT: F 12 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7455 (tt) REVERT: F 15 LYS cc_start: 0.8745 (tttt) cc_final: 0.8365 (tttm) REVERT: F 74 ASP cc_start: 0.8764 (t0) cc_final: 0.8449 (t0) REVERT: F 102 PRO cc_start: 0.7535 (Cg_endo) cc_final: 0.7190 (Cg_exo) REVERT: F 103 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.5174 (mmp80) outliers start: 32 outliers final: 17 residues processed: 98 average time/residue: 0.0740 time to fit residues: 9.0719 Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 32 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.159814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132397 restraints weight = 4803.049| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.15 r_work: 0.3653 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4350 Z= 0.206 Angle : 0.577 6.830 5922 Z= 0.307 Chirality : 0.050 0.152 708 Planarity : 0.004 0.029 726 Dihedral : 5.006 19.289 588 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.34 % Allowed : 19.66 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.019 0.002 TYR A 114 PHE 0.011 0.002 PHE D 95 TRP 0.007 0.002 TRP A 79 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 ( 4350) covalent geometry : angle 0.57700 / 0.31 ( 5922) hydrogen bonds : bond 0.01931 / 1.26 ( 63) hydrogen bonds : angle 4.65946 / 3.23 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.098 Fit side-chains REVERT: D 13 MET cc_start: 0.6698 (mmm) cc_final: 0.6316 (tpp) REVERT: D 85 SER cc_start: 0.8848 (t) cc_final: 0.8533 (p) REVERT: A 12 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6842 (tt) REVERT: A 15 LYS cc_start: 0.8776 (tttt) cc_final: 0.8242 (ttmt) REVERT: B 13 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.6899 (tmm) REVERT: B 58 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7432 (mp) REVERT: E 63 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7104 (tp30) REVERT: F 12 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (tt) REVERT: F 15 LYS cc_start: 0.8727 (tttt) cc_final: 0.8274 (tttm) REVERT: F 74 ASP cc_start: 0.8737 (t0) cc_final: 0.8236 (t0) REVERT: F 76 LYS cc_start: 0.8746 (mppt) cc_final: 0.8332 (mptt) REVERT: F 102 PRO cc_start: 0.7705 (Cg_endo) cc_final: 0.7377 (Cg_exo) REVERT: F 103 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.4956 (mmp80) outliers start: 25 outliers final: 13 residues processed: 94 average time/residue: 0.0733 time to fit residues: 8.5367 Evaluate side-chains 92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 52 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.129822 restraints weight = 4971.314| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.97 r_work: 0.3602 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 4350 Z= 0.339 Angle : 0.692 7.670 5922 Z= 0.369 Chirality : 0.053 0.153 708 Planarity : 0.005 0.047 726 Dihedral : 5.433 20.798 588 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 5.77 % Allowed : 20.51 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 104 TYR 0.025 0.002 TYR A 114 PHE 0.013 0.003 PHE D 87 TRP 0.010 0.002 TRP F 79 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00784 / 0.34 ( 4350) covalent geometry : angle 0.69225 / 0.37 ( 5922) hydrogen bonds : bond 0.02135 / 1.47 ( 63) hydrogen bonds : angle 4.72404 / 3.34 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.087 Fit side-chains REVERT: D 85 SER cc_start: 0.8925 (t) cc_final: 0.8649 (p) REVERT: A 12 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7002 (tt) REVERT: B 13 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7000 (tpp) REVERT: B 58 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7464 (mp) REVERT: E 63 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: F 12 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7482 (tt) REVERT: F 15 LYS cc_start: 0.8740 (tttt) cc_final: 0.8322 (ttmt) REVERT: F 74 ASP cc_start: 0.8843 (t0) cc_final: 0.8564 (t0) REVERT: F 102 PRO cc_start: 0.7873 (Cg_endo) cc_final: 0.7632 (Cg_exo) REVERT: F 103 ARG cc_start: 0.7447 (mtm-85) cc_final: 0.5171 (mmp80) outliers start: 27 outliers final: 21 residues processed: 89 average time/residue: 0.0478 time to fit residues: 5.3159 Evaluate side-chains 99 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.166607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141429 restraints weight = 4895.110| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.86 r_work: 0.3759 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4350 Z= 0.123 Angle : 0.516 6.185 5922 Z= 0.272 Chirality : 0.049 0.139 708 Planarity : 0.003 0.019 726 Dihedral : 4.725 19.324 588 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.06 % Allowed : 22.22 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 104 TYR 0.014 0.001 TYR A 114 PHE 0.008 0.001 PHE D 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 4350) covalent geometry : angle 0.51597 / 0.27 ( 5922) hydrogen bonds : bond 0.01401 / 0.90 ( 63) hydrogen bonds : angle 4.44405 / 3.02 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.088 Fit side-chains REVERT: D 85 SER cc_start: 0.8803 (t) cc_final: 0.8420 (p) REVERT: A 12 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.6984 (tt) REVERT: B 13 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6958 (tpp) REVERT: B 58 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7463 (mp) REVERT: C 103 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.5432 (ptt-90) REVERT: E 63 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7142 (tp30) REVERT: E 104 ARG cc_start: 0.7231 (ttm-80) cc_final: 0.6963 (mtt180) REVERT: F 15 LYS cc_start: 0.8586 (tttt) cc_final: 0.8133 (ttmt) REVERT: F 69 TYR cc_start: 0.8864 (m-80) cc_final: 0.8576 (m-80) REVERT: F 74 ASP cc_start: 0.8703 (t0) cc_final: 0.8115 (t0) REVERT: F 76 LYS cc_start: 0.8709 (mppt) cc_final: 0.8383 (mptt) REVERT: F 103 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.5118 (mmp80) outliers start: 19 outliers final: 9 residues processed: 82 average time/residue: 0.0545 time to fit residues: 5.6746 Evaluate side-chains 82 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.0770 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 overall best weight: 3.7144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132006 restraints weight = 4864.265| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.15 r_work: 0.3681 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4350 Z= 0.186 Angle : 0.568 6.097 5922 Z= 0.298 Chirality : 0.049 0.138 708 Planarity : 0.004 0.078 726 Dihedral : 4.870 19.952 588 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.49 % Allowed : 21.37 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 104 TYR 0.020 0.002 TYR A 114 PHE 0.010 0.002 PHE D 95 TRP 0.004 0.001 TRP C 79 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 4350) covalent geometry : angle 0.56783 / 0.30 ( 5922) hydrogen bonds : bond 0.01550 / 1.05 ( 63) hydrogen bonds : angle 4.33571 / 3.00 ( 189) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.137 Fit side-chains REVERT: D 85 SER cc_start: 0.8882 (t) cc_final: 0.8536 (p) REVERT: A 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6940 (tt) REVERT: B 13 MET cc_start: 0.7602 (tmm) cc_final: 0.7055 (tpp) REVERT: B 58 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7455 (mp) REVERT: B 107 ILE cc_start: 0.6657 (mm) cc_final: 0.5909 (pt) REVERT: C 103 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.5389 (ptt-90) REVERT: E 63 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: E 104 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.7069 (mtt180) REVERT: F 15 LYS cc_start: 0.8627 (tttt) cc_final: 0.8192 (ttmt) REVERT: F 69 TYR cc_start: 0.8910 (m-80) cc_final: 0.8666 (m-80) REVERT: F 74 ASP cc_start: 0.8744 (t0) cc_final: 0.8244 (t0) REVERT: F 76 LYS cc_start: 0.8761 (mppt) cc_final: 0.8470 (mptt) REVERT: F 103 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.5243 (mmp80) outliers start: 21 outliers final: 15 residues processed: 88 average time/residue: 0.0805 time to fit residues: 8.7870 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 58 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 0.0370 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.163549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137359 restraints weight = 4801.607| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.98 r_work: 0.3700 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4350 Z= 0.165 Angle : 0.548 5.649 5922 Z= 0.288 Chirality : 0.049 0.136 708 Planarity : 0.004 0.065 726 Dihedral : 4.775 19.628 588 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.13 % Allowed : 20.30 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.019 0.001 TYR A 114 PHE 0.009 0.002 PHE D 95 TRP 0.003 0.001 TRP C 79 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 4350) covalent geometry : angle 0.54772 / 0.29 ( 5922) hydrogen bonds : bond 0.01443 / 0.97 ( 63) hydrogen bonds : angle 4.27296 / 2.95 ( 189) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 0.146 Fit side-chains REVERT: D 85 SER cc_start: 0.8868 (t) cc_final: 0.8496 (p) REVERT: A 12 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6990 (tt) REVERT: B 13 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7037 (tpp) REVERT: B 58 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 63 GLU cc_start: 0.8153 (pt0) cc_final: 0.7916 (pm20) REVERT: B 107 ILE cc_start: 0.6623 (mm) cc_final: 0.5842 (pt) REVERT: C 103 ARG cc_start: 0.7428 (mtm-85) cc_final: 0.5400 (ptt-90) REVERT: E 63 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: F 13 MET cc_start: 0.7150 (tmm) cc_final: 0.6828 (tmm) REVERT: F 15 LYS cc_start: 0.8646 (tttt) cc_final: 0.8269 (tttm) REVERT: F 69 TYR cc_start: 0.8882 (m-80) cc_final: 0.8642 (m-80) REVERT: F 74 ASP cc_start: 0.8718 (t0) cc_final: 0.8146 (t0) REVERT: F 76 LYS cc_start: 0.8771 (mppt) cc_final: 0.8447 (mptt) REVERT: F 103 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.5350 (mmp80) outliers start: 24 outliers final: 18 residues processed: 87 average time/residue: 0.0557 time to fit residues: 6.1225 Evaluate side-chains 92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.163406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.137076 restraints weight = 4863.365| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.95 r_work: 0.3700 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4350 Z= 0.170 Angle : 0.548 5.602 5922 Z= 0.290 Chirality : 0.049 0.136 708 Planarity : 0.004 0.059 726 Dihedral : 4.791 19.878 588 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.34 % Allowed : 20.51 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 104 TYR 0.020 0.002 TYR A 114 PHE 0.009 0.002 PHE D 95 TRP 0.004 0.001 TRP A 79 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 4350) covalent geometry : angle 0.54797 / 0.29 ( 5922) hydrogen bonds : bond 0.01456 / 0.99 ( 63) hydrogen bonds : angle 4.26577 / 2.97 ( 189) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.087 Fit side-chains REVERT: D 85 SER cc_start: 0.8860 (t) cc_final: 0.8492 (p) REVERT: A 12 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6966 (tt) REVERT: B 13 MET cc_start: 0.7469 (tmm) cc_final: 0.7127 (tpp) REVERT: B 58 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7479 (mp) REVERT: B 63 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: B 107 ILE cc_start: 0.6547 (mm) cc_final: 0.5832 (pt) REVERT: C 103 ARG cc_start: 0.7422 (mtm-85) cc_final: 0.5375 (ptt-90) REVERT: E 63 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: F 13 MET cc_start: 0.7138 (tmm) cc_final: 0.6809 (tmm) REVERT: F 15 LYS cc_start: 0.8647 (tttt) cc_final: 0.8159 (ttmt) REVERT: F 69 TYR cc_start: 0.8869 (m-80) cc_final: 0.8646 (m-80) REVERT: F 74 ASP cc_start: 0.8719 (t0) cc_final: 0.8197 (t0) REVERT: F 76 LYS cc_start: 0.8761 (mppt) cc_final: 0.8455 (mptt) REVERT: F 103 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.5357 (mmp80) outliers start: 25 outliers final: 19 residues processed: 88 average time/residue: 0.0450 time to fit residues: 4.9900 Evaluate side-chains 91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.0020 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 overall best weight: 2.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.165492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139234 restraints weight = 4788.172| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.94 r_work: 0.3733 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4350 Z= 0.143 Angle : 0.529 5.418 5922 Z= 0.280 Chirality : 0.049 0.132 708 Planarity : 0.004 0.064 726 Dihedral : 4.667 19.316 588 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.70 % Allowed : 20.73 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.34), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.017 0.001 TYR A 114 PHE 0.008 0.001 PHE D 95 TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 ( 4350) covalent geometry : angle 0.52863 / 0.28 ( 5922) hydrogen bonds : bond 0.01358 / 0.91 ( 63) hydrogen bonds : angle 4.23576 / 2.93 ( 189) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.113 Fit side-chains REVERT: D 85 SER cc_start: 0.8839 (t) cc_final: 0.8451 (p) REVERT: A 12 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6949 (tt) REVERT: B 13 MET cc_start: 0.7415 (tmm) cc_final: 0.7141 (tpp) REVERT: B 58 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7475 (mp) REVERT: B 63 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: C 76 LYS cc_start: 0.8620 (mppt) cc_final: 0.8299 (mppt) REVERT: C 103 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.5322 (ptt-90) REVERT: E 63 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: F 13 MET cc_start: 0.7071 (tmm) cc_final: 0.6744 (tmm) REVERT: F 15 LYS cc_start: 0.8654 (tttt) cc_final: 0.8157 (ttmt) REVERT: F 69 TYR cc_start: 0.8865 (m-80) cc_final: 0.8642 (m-80) REVERT: F 74 ASP cc_start: 0.8701 (t0) cc_final: 0.8205 (t0) REVERT: F 76 LYS cc_start: 0.8741 (mppt) cc_final: 0.8450 (mptt) REVERT: F 103 ARG cc_start: 0.7335 (mtm-85) cc_final: 0.5300 (mmp80) outliers start: 22 outliers final: 18 residues processed: 84 average time/residue: 0.0486 time to fit residues: 5.1181 Evaluate side-chains 91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 63 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 23 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.158374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.131322 restraints weight = 4895.963| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.01 r_work: 0.3625 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 4350 Z= 0.295 Angle : 0.647 5.998 5922 Z= 0.346 Chirality : 0.052 0.141 708 Planarity : 0.005 0.067 726 Dihedral : 5.173 21.053 588 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.56 % Allowed : 20.73 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.33), residues: 522 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 104 TYR 0.025 0.002 TYR A 114 PHE 0.012 0.003 PHE B 33 TRP 0.009 0.002 TRP A 79 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.30 ( 4350) covalent geometry : angle 0.64734 / 0.35 ( 5922) hydrogen bonds : bond 0.01817 / 1.28 ( 63) hydrogen bonds : angle 4.43823 / 3.14 ( 189) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 899.60 seconds wall clock time: 16 minutes 7.71 seconds (967.71 seconds total)